To give ethers and potions to the flowers in Wonderland you need to use the same menu as if you are about to use an item on yourself. Once you are close enough to auto-target the flower then it will become a choice in your “party” menu.
This appears after you open the item menu and select an item to use. Typically the options will only include yourself and your other 2 party members. The flower will appear at the very bottom, and you merely select its name to use the item. Pretty neat!